rs285875

Positions:

• chr8-105043358-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.907 in 152,204 control chromosomes in the GnomAD database, including 62,728 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.91 (62728 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.105043358T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000518180.1	n.242+51689T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137933 AN: 152086 Hom.: 62689 Cov.: 32

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.901

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.907 AC: 138026 AN: 152204 Hom.: 62728 Cov.: 32 AF XY: 0.911 AC XY: 67789 AN XY: 74420

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.902

Alfa AF: 0.897 Hom.: 7902

Bravo AF: 0.906

Asia WGS AF: 0.952 AC: 3306 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs285875; hg19: chr8-106055586;